Daniel:Notebook/GenomeMiner/2013-10-15

From ZhangLabWiki
Jump to navigation Jump to search

HL155 Novoalign (Started 10/3/2013)

Back to Calendar

V4S1 Novoalign (Changing Index Length)

Attempting to fix these issues with Novoalign by changing the k-mer length when creating the index.

Pipeline

novoindex -k 98 index_V4S1_fullrevcomp.ndx V4S1_fullrevcomp.fa
novoalign -d index_V4S1_fullrevcomp.ndx -f ../../s_2_1_Indx13.txt -F ILMFQ -r ALL -o SAM > v4s1_novo.sam
the rest of the bash script

Alignment Results

#     Read Sequences: 11450664
#            Aligned:  4194879
#   Unique Alignment:  4178621
#   Gapped Alignment:  3042944
#     Quality Filter:    23301
# Homopolymer Filter:       40
#       Elapsed Time: 9373.277 (sec.)
#           CPU Time: 154.0 (min.)
# Done at Tue Oct 15 16:24:52 2013

Error Counting Results

Error Rate: 6.63%
Error Rate of Insertions: .179%
Error Rate of Deletions: 2.36%
Error Rate of Substitutions: 4.09%

So no, that really didn't do much. I'll look into other options with novoalign to try and correct the error, or I'll do some post-processing.